A modular pipeline for natural language processing-screened human abstraction of a pragmatic trial outcome from electronic health records.

Abstract

Background: Natural language processing allows efficient extraction of clinical variables and outcomes from electronic health records (EHRs). However, measuring pragmatic clinical trial outcomes may demand accuracy that exceeds natural language processing performance. Combining natural language processing with human adjudication can address this gap, yet few software solutions support such workflows. We developed a modular, scalable system for natural language processing-screened human abstraction to measure the primary outcomes of two clinical trials.

Methods: In two clinical trials of hospitalized patients with serious illness, a deep-learning natural language processing model screened electronic health record passages for documented goals-of-care discussions. Screen-positive passages were referred for human adjudication using a REDCap-based system to measure the trial outcomes. Dynamic pooling of passages using structured query language within the REDCap database reduced unnecessary abstraction while ensuring data completeness.

Results: In the first trial (N = 2512), natural language processing identified 22,187 screen-positive passages (0.8%) from 2.6 million electronic health record passages. Human reviewers adjudicated 7494 passages over 34.3 abstractor-hours to measure the cumulative incidence and time to first documented goals-of-care discussion for all patients with 92.6% patient-level sensitivity. In the second trial (N = 617), natural language processing identified 8952 screen-positive passages (1.6%) from 559,596 passages at a threshold with near-100% sensitivity. Human reviewers adjudicated 3509 passages over 27.9 abstractor-hours to measure the same outcome for all patients.

Discussion: We present the design and source code for a scalable and efficient pipeline for measuring complex electronic health record-derived outcomes using natural language processing-screened human abstraction. This implementation is adaptable to diverse research needs, and its modular pipeline represents a practical middle ground between custom software and commercial platforms.